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Sample GSM4023772 Query DataSets for GSM4023772
Status Public on Feb 24, 2021
Title DMSO_TAM_A
Sample type SRA
 
Source name DMSO_TAM
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: Mutant RNF40RosaCreERT2 mouse
cell type: Primary Calvarial Osteoblasts
treatment: for 7 d with 250nM 4-hydroxytamoxifen, and then for additional 7 days with DMSO
library prep kit: TruSeq RNA Smaple Prep Kit-v2, Illumina
Treatment protocol For induction of RNF40 knockout, the cells were treated with 250nM of 4-hydroxytamoxifen or equivalent volume of vehicle (ethanol). For differentiation, cells were treated with 5 mM β-glycerophosphate and 0.2 mM ascorbate. For vitamin D studies, cells were treated for 7 days with 10nM calcitriol or equal volume of vehicle (DMSO).
Growth protocol Mouse calvarial osteoblasts were maintained in aMEM complete media with 10% FBS and 1% P/S
Extracted molecule total RNA
Extraction protocol The total cell RNA was isolated with standard TRIzol extraction protocol
4 µg of total cell RNA was used for library preparation with NEXTflex Rapid Directional mRNA-Seq from Bioo Scientific and 500ng of total cell RNA was used for library preparation with TruSeq RNA Smaple Prep Kit-v2 following manufacturers' protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing The FASTQ files were mapped to the mouse mm9 genome using TopHat Gapped-read mapper for RNA-seq data with very-sensitive BOWTIE2 settings. The differential analysis was performed by using Cuffdiff with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: The provided mRNA-Seq analysis files present the differentially regulated genes between the indicated conditions in excel file format.
 
Submission date Aug 09, 2019
Last update date Feb 24, 2021
Contact name Steven A. Johnsen
Organization name Robert Bosch Center for Tumor Diseases
Lab Molecular Cancer Epigenetics
Street address Auerbachstraße 112
City Stuttgart
State/province BW
ZIP/Postal code 70376
Country Germany
 
Platform ID GPL21103
Series (2)
GSE135628 RNF40 exerts stage-dependent functions in differentiating osteoblasts and is essential for bone cell crosstalk [RNA-seq]
GSE135629 RNF40 exerts stage-dependent functions in differentiating osteoblasts and is essential for bone cell crosstalk
Relations
BioSample SAMN12542666
SRA SRX6686951

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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